iTunes has taken to building playlists (and starting to play them) from any .m3u files it finds while importing media folders. It isn't clear yet whether this behavior is supposed to be a new "feature" or has been accidentally introduced, but importing folders that contain .m3u files may not give the results you are used to.
iTunes Folder Watch would work well if your current workflow is to have iTunes scan the media folder for new files, since it only adds the file types you want it to. However if you are specifically adding individual folders then, at least for now, you probably need to remove the .m3u files or edit their extentions before importing.
On the other hand, if you don't need the playlist files then throw them away. Use the search tool in Windows Explorer to find files of the form *.m3u in your media folders, select them all with Ctrl-A and then delete.